On Mon, Dec 2, 2013 at 11:53 AM, Michal Krompiec
<[email protected]>wrote:
> But does CombineMols create any new bonds?
>
It does not, but you can add bonds by converting to an EditableMol and
working there.
Something like this:
In [2]: m = Chem.MolFromSmiles('c1ccccc1N')
In [3]: m2 = Chem.MolFromSmiles('CC(=O)')
In [4]: cm = Chem.CombineMols(m,m2)
In [5]: em = Chem.EditableMol(cm)
In [6]: em.AddBond(6,8,Chem.BondType.SINGLE)
Out[6]: 10
In [7]: nm = em.GetMol()
In [8]: Chem.SanitizeMol(nm)
Out[8]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [10]: print Chem.MolToSmiles(nm)
CC(=O)Nc1ccccc1
What is the simplest/fastest way of joining two molecules (fragments)
> together? (i.e. is there anything simpler than using
> ReplaceSubstructs)
>
Both "fastest" and "simplest" are tough to assess. It really depends on
what your starting point is.
ReplaceSubstructs() is designed for the very simple case of replacing a
piece of the molecule that is connected via one bond. It has the
significant limitation that it (currently) assumes that the bond will be
formed to the first atom in the replacement.
CombineMols() is for combining two fragments into a single new molecule
with an optional rigid displacement of the second molecule's conformations.
No bonds are formed.
Either of the above two preserve any conformation information that exists
on the input molecules.
The most general and flexible approach to this is almost definitely to use
reactions. However, these are somewhat trickier to encode and do not
preserve conformations.
-greg
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